AMBER Archive (2004)

Subject: RE: AMBER: pbsa calculation on part of the molecule & nmode analysis

From: S. Frank Yan (SYan_at_gnf.org)
Date: Thu May 20 2004 - 20:06:11 CDT

Thanks for the reply. Even the system was only partially solvated
around active site during MD simulation for exploring different
conformations of both ligand and the surrounding protein residues, in
the salvation free energy calculation it may be still valid to use the
whole system to carry out pbsa calculation, since the residues outside
the core region are fixed, hoping the effects may be cancelled out. In
addition, pbsa calculation is relatively fast, it is affordable to do
that.

However, in the normal mode analysis, it is usually not affordable to
carry out the analysis for the entire complex. Do we just truncate the
residues in the core region and carry out the normal mode analysis?

Thanks,
Frank

> -----Original Message-----
> From: Ray Luo [mailto:rluo_at_uci.edu]
> Sent: Wednesday, May 19, 2004 1:32 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: pbsa calculation on part of the molecule
>
> Group input has never been tested in pbsa. An issue also unclear in
> these types of calculations is how we should treat the environment
> outside the selected residues: bulk water or rest of the protein?
>
> If the environment is bulk water, you can just truncate the selected
> residues by yourself and regenerate a prmtop file for a separate pbsa
> run. If the environment is the rest of the protein, you need to wait
for
> the next update of pbsa coming out later this year.
>
> Best,
> Ray
>
> S. Frank Yan wrote:
>
> >Hi,
> >
> >I was wondering if there's a way to carry out the PBSA calculation on
> >part of the molecule, like within 20 angstrom of the active site.
This
> >most likely results from belly simulation of a partially solvated
> >system. I tried to set the group in pbsa input, but the error
message
> >is:
> >
> >....
> >GRP 1 RES 190 TO 206
> > Number of atoms in this group = 2696
> > ----- END OF GROUP READ -----
> > When igb>0, the moving part must be at the
> > start of the molecule. This does not seem
> > to be the case here.
> > natbel,i,igroup(i) = 2696 2757
> > 1
> >
> >Thanks a lot,
> >Frank
> >
>
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> >
> >
> >
>
>
> --
> ====================================================
> Ray Luo, Ph.D.
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
> Office: (949)824-9528 Lab: (949)824-9562
> Fax: (949)824-8551 e-mail: rluo_at_uci.edu
> Home page: http://rayl0.bio.uci.edu/rayl/
> ====================================================
>
>
>
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